I just noticed that "revision 2309 : Email alert reduced volume" on the development blog. Which reminded me of another long standing "Oh, I should probably mention <that> sometime".

The immediate thought was about game volume(s). But there are some others too.
I'd regard all these as nice to have. The volume controls would be my highest priority item. Then the "invert camera direction" toggle.
But as always, it's your game - so you're choices. These are just my suggestions.

Video:

I know lots of people go ape about visual settings. Not me.
But one nice feature would be monitor selection. I personally run with 2 monitors (1920x1200 + 1920x1080). I've heard video pundits be mildly impressed by games that include a primary monitor picker. I wouldn't miss it if it weren't added, but since some people regard it as an impressive feature for modern games to have - I thought I'd list it.

Personally, I'd like to see a second sets of keybindings per game action. It's very much "icing on the cake", but it's also one of the indicators I look for in a "quality game". Whilst it's no longer the case, my brother and I used to share a computer - he's left handed, I'm right handed. That's just one example where double keybinds are invaluable.

I've already raised this as a suggestion in it's own right, but: a "reverse mouse/camera rotation" toggle. The current <MMB>+<Mouse drag> rotate the camera in the wrong direction for me. I know not everyone would agree. But I'd like to be able to set it to account for my preferences.

An old school option that nobody includes any more: Enable/Disable screen edge movement. Personally it's not something I would ever disable, but I can see why players might want to. The option would disable the game world scrolling up/down/left/right when the cursor nudges the edge of the game screen. Most of the UI elements are near the edges and sometimes I find myself inadvertently scrolling when I moved the mouse a little too far. Anyway, it's another "quality" option that I can't imagine would be too difficult to add.